[Vegan-commits] r569 - in pkg: R man

[noreply at r-forge.r-project.org]

Author: psolymos
Date: 2008-11-16 19:41:23 +0100 (Sun, 16 Nov 2008)
New Revision: 569

Modified:
   pkg/R/permatswap.R
   pkg/man/permatfull.Rd
Log:
match.arg bug fixed (reported by JO)


Modified: pkg/R/permatswap.R
===================================================================
--- pkg/R/permatswap.R	2008-11-16 17:43:44 UTC (rev 568)
+++ pkg/R/permatswap.R	2008-11-16 18:41:23 UTC (rev 569)
@@ -77,7 +77,7 @@
     count <- mtype == "count"
     if (count) {
         method <- match.arg(method, c("swap", "quasiswap"))
-    } else {method <- match.arg(method, c("swap", "quasiswap", "tswap", "quasiswap"))}
+    } else {method <- match.arg(method, c("swap", "quasiswap", "tswap", "backtracking"))}
 
     m <- as.matrix(m)
     n.row <- nrow(m)

Modified: pkg/man/permatfull.Rd
===================================================================
--- pkg/man/permatfull.Rd	2008-11-16 17:43:44 UTC (rev 568)
+++ pkg/man/permatfull.Rd	2008-11-16 18:41:23 UTC (rev 569)
@@ -35,7 +35,7 @@
   \item{hab}{numeric vector or factor with length same as \code{nrow(m)} for grouping rows within strata (habitat classes) for restricted permutations. Unique values or levels are used.}
   \item{mtype}{matrix data type, either \code{"count"} for count data, or \code{"prab"} for presence-absence type incidence data.}
   \item{times}{number of permuted matrices.}
-  \item{method}{character for method used for the swap algorithm (\code{"swap"}, \code{"tswap"}, \code{"quasiswap"}, \code{"backtrack"}) as described for function \code{\link{commsimulator}}. If \code{mtype="count"} the \code{"quasiswap"} and \code{"swap"} methods are available.}
+  \item{method}{character for method used for the swap algorithm (\code{"swap"}, \code{"tswap"}, \code{"quasiswap"}, \code{"backtrack"}) as described for function \code{\link{commsimulator}}. If \code{mtype="count"} the \code{"quasiswap"} and \code{"swap"} methods are available (see details).}
   \item{shuffle}{character, indicating whether individuals (\code{"ind"}), samples (\code{"samp"}) or both (\code{"both"}) should be shuffled, see details.}
   \item{burnin}{number of null communities discarded before proper analysis in sequential (\code{"swap", "tswap"}) methods.}
   \item{thin}{number of discarded permuted matrices between two evaluations in sequential (\code{"swap", "tswap"}) methods.}